Mutation Mechanisms Leading to Malignant Transformation, Including Chromosomal Translocation and Point Mutations

Division Of Clinical Sciences - Nci

Investigators

Linked publications, trials & patents

Abstract

It is well-established that many leukemias are initially sensitive to chemotherapy, but ultimately develop resistance. We have generated a panel of T-ALL cell lines, and have generated chemotherapy-resistatn derivatives of these cell lines, through continued growth in the presence of chemotherapy agents. The chemotherapy resistant cell lines have been assayed for acquired single nucleotide variants (SNV), copy number aberrations (CNA), and RNA transcription changes in order to identify important events in developing chemotherapy resistance. Initial results from this study identified focal, pronounced (>20-fold) copy number gains of Dhfr and Abcb1a (previously designated MDR1) associated with resistance to methotrexate and vincristine respectively. Surprisingly, we found that inactivation of deoxcytidine kinase (Dck), which is required for cytidine and cytarabine phosphorylation, led not only to cytarabine resistance, but to a novel, previously unrecognized mutation signature. We have developed a novel in vitro assay (designated GEMINI, for Genotoxic Mutational Signature Identified After Clonal Expansion In Vitro) to study this novel mutation signature in more detail. We have determined that this signature persists even after treatment with the inciting agent (cytarabine) is removed, suggesting that the mutational signature was initiated by one or more acquired mutations in the cytarabine treated subclones. Further study has demonstrated that the mutational signature can be divided into at least three separate components, one of these seems to be related to Trp53 mutation, and a second component is associated with rate of cell division. These results have been published in abstract form, and we plan to submit a manuscript detailing these findings in late FY2025. As described in Project 1, we have identified mutagenic properties of both novel and FDA approved azanucleosides. We have published one manuscript documenting these mutations in FY2025 (PMID: 40681875), and a second manuscript highlighting the mechanisms which produce these mutations is in press. More recently, we have identified recurrent mutations in mitochondrial DNA (mtDNA) produced after treatment with specific chemotherapy agents. These mutations in mtDNA have important similarities as well as distinguishing features in mtDNA vs nuclear DNA. For instance, azanucleoside treatment induces G > C mutations in both nuclear DNA and mtDNA, however, the G > C mutations in nuclear DNA occur predominantly in a CpG context and are not strand specific, while mutations in mtDNA are in a non-CpG context and are strand specific. We plan to submit a manuscript describing these findings in late FY2025.